It opens with a boy being chased by robots into a museum where he discovers the deactivated body of Atom hanging in a display case. Due to the actions of the robots chasing the boy, or an electrical storm raging outside of the building, a bolt of lighting sets off an explosion in the display area, knocking Atom over and reactivating him. Atom saves the boy from his pursuers, only to run out of power.

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The boy manages to carry Atom to a waiting submarine where an older version of Dr. Ochanomizu is waiting. ​ It appears that he is the boy's guardian. ​ The submarine is then chased by robots that look like they came right out of the Matrix. ​ Eventually they confront an A.I. that seems to be in control of the robots, at which point Atom wakes up from a dream back in the early 21st century with Uran and Dr. O'​Shay.